BACKGROUND: the fecal pancreatic elastase-1 (EL-1) test is a new non-invasive test for pancreatic function. The aim of the study was to evaluate the intra-patient variability of the fecal EL-1 test in a cystic fibrosis (CF) population. METHODS: 26 CF patients were recruited. Mean patient (S.D.) age was 13.7 years (5.39). Nineteen patients had classical pancreatic insufficiency (PI) based on a clinical syndrome of malabsorption plus steatorrhea on a 72 h fecal fat balance. They were all treated with enzyme supplements. Four patients had classical pancreatic sufficiency (PS): no symptoms of malabsorption, no steatorrhea on a 72 h fecal fat balance, no enzyme treatment. Two patients had symptoms suggestive of PI but had a normal 72 h fecal fat balance: (doubtful pancreatic status (PD)). The CF patients were asked to collect stool samples on 7 consecutive days. EL-1 content in the samples was measured in duplicate. A cut-off of 200 microgEL-1/g stool was used for diagnosing PI. RESULTS: mean intra-assay variability was 4.06%. All PI patients had EL-1 levels below detection limit. For the PS group maximal intra-patient variability was 35%, one stool sample EL-1 level was below the 200-microg cut-off. In the PD group the maximal intra-patient variability was 37% and EL-1 levels were inconclusive for the diagnosis of PI in both patients. CONCLUSIONS: the EL-1 test can be used for diagnosing severe PI in CF patients with overt clinical symptoms of malabsorption. However, in CF patients where the clinical picture is less clear the EL-1 test may be inconclusive due to significant intra-patient variability.